find transcription factor binding sites for a list of genes

Hi All,

I’ve been trying to find a web-based resource for identifying potential transcription factor binding sites in the promoters of a list of genes from
a RNAseq experiment. I’m looking for a way to input a list of gene names and then get a list of transcription factors whose predicted binding
sites are enriched in the promoters of those genes.

It seems that many tools are optimized for analyzing only one promoter at a time or that they don’t have information
on C. elegans promoters. I’ve played with Opossum, but it only searches for binding sites for a handful of worm transcription factors. Genomatix
doesn’t seem to be able to produce a list of enriched transcription factor binding sites. I know that TRANSFAC is widely used, but, again, I’m not
sure how well it would handle a large list of genes.

Can anyone recommend another resource that’s designed to perform the type of analysis that I’m looking for?

Many thanks!

Have you considered the modENCODE resource? They aim to tackle these types of problems.

Regulatory Sequence Analysis Tools (RSAT). As the site says, it “provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences”.